Data Science in the Time of Coronavirus

# Data Science in the Time of Coronavirus
## Storytelling using the Data Science Platform
### Srikanth Aravamuthan
### University of Wisconsin-Madison
### January 17, 2024

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# Background & Research

<img src="profile-picture-1.jpg" width="100%">

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- Graduate Student in Comparative Biomedical Sciences

- Background in Math & Science

- Research in Computer Vision

- Consulting Work in Statistics, Biostatistics, Computer Science

- Contact: aravamuthan@wisc.edu

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]

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# Overview

- **COVID-19 Data Visualizations**

- COVID-19 Growth Rates in Wisconsin
  - Geofaceting Instantaneous R<sub>0</sub>
  - COVID-19 Activity Level in Wisconsin
  - SARS-CoV-2 Screening Strategies
  - Nowcast COVID-19 Cases and Hospitalizations

- **Automate DairyCOMP 305**

- **Update DDCheck App**

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# COVID-19 Data Visualizations of Descriptive Statistics

Sean Kent, Steve Goldstein, and Brian Yandell (University of Wisconsin-Madison)

Juan Francisco Mandujano Reyes & D&ouml;rte D&ouml;pfer (University of Wisconsin-Madison)

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# New York Times Data Visualizations

.pull-left[
  <center>
  <img src="data:image/png;base64,#nyt-upshot-headline.png" alt="diagonal layout" width="60%" border = "1"/>
  <img src="data:image/png;base64,#nyt-upshot-growth-rate-vs-time.png" alt="diagonal layout" width="60%" border = "1"/>
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.pull-right[
  <center>
    <img src="data:image/png;base64,#nyt-upshot-metro-box.png" alt="diagonal layout" width="60%" border = "1"/>
    <img src="data:image/png;base64,#nyt-upshot-growth-rate-vs-cases.png" alt="diagonal layout" width="60%" border = "1"/>
  </center>
  </br>
  <div style="width:300; word-wrap: break-word;">
    <https://www.nytimes.com/interactive/2020/04/03/upshot/coronavirus-metro-area-tracker.html>
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# COVID-19 Growth Rates in Wisconsin

"*Wisconsin leaders need information about the extent and impact of COVID-19 to make good decisions.*" - **AFI DSI COVID-19 Research Group Charter**

"*Can we add value with visualizations of growth rates in Wisconsin metro areas?*" - **Steve Goldstein**

**Audience**:
- Wisconsin public health officials
- Health system officials
- Interested modelers and citizens

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# COVID-19 Growth Rates in Wisconsin

.pull-left[
  <center>
  <img src="daily-growth-rate.png" height="200" border = "1">
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  <img src="map-metro-areas-cases.png" height="200" border = "1">
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  <center>
  <img src="growth-rate-case-count.png" height="200" border = "1">
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  <img src="map-metro-areas-deaths.png" height="200" border = "1">
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.center[
  </br>
  [data-viz.it.wisc.edu/wi-metro-growth-rate/](https://data-viz.it.wisc.edu/wi-metro-growth-rate/)
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# COVID-19 Growth Rates in Wisconsin

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  <center>
  <img src="new-cases-case-count.png" width="100%" border = "1">
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  <center>
  <img src="new-cases-case-count-per-capita.png" width="100%" border = "1">
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# Publish Document or Website

- [data-viz.it.wisc.edu/wi-metro-growth-gundersen/](https://data-viz.it.wisc.edu/wi-metro-growth-gundersen/)
- [data-viz.it.wisc.edu/wi-metro-growth-marshfield/](https://data-viz.it.wisc.edu/wi-metro-growth-marshfield/)

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- Daily updates to new data
- Customized to the needs of the heath system

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# Posit Connect Deployment

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- Standalone publishing platform
  - Dashboards
  - On-demand and scheduled reports
  - Interactive applications

- User-friendly web application
  - Access controls
  - Performance settings
  - View logs

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# Geofaceting Instantaneous R<sub>0</sub>

**Project Idea**: "*Can we summarize `\(R_0\)` spatially and temporally for all Wisconsin counties over all time points.*"

**Audience**:
- Wisconsin public health officials
- Interested modelers

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# Geofaceting Instantaneous R<sub>0</sub>

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- Preserves the geographical orientation

- Maintains the time dependence

- Won honorable mention in John Hunter Excellence in Plotting Competition at SciPy 2020

- Website: [data-viz.it.wisc.edu/instantaneous-r0-geofacet-wi-county/](https://data-viz.it.wisc.edu/instantaneous-r0-geofacet-wi-county/)

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# COVID-19 Activity Level in Wisconsin

**Project Idea**:
- It would be helpful to overlay HERC regions on the county map
- It would be helpful to view the census track level map
- It would be helpful to see the time course

**Audience**:
- Wisconsin public health officials
- Health system officials
- Interested modelers and citizens

]

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# COVID-19 Activity Level in Wisconsin

.pull-left[
  <center>
  <img src="dhs-herc-regions.png" height="200" border = "1">
  </br>
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  <img src="map-anim.png" height="200" border = "1">
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  <img src="dhs-covid-19-activity-level.png" height="200" border = "1">
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# SARS-CoV-2 Screening Strategies

.pull-left[
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  <img src="data:image/png;base64,#paltiel-paper.png" width = "100%" border = "1"/>
  <img src="data:image/png;base64,#larremore-paper.png" width = "100%" border = "1"/>
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  </br>
  <div style="width:300; word-wrap: break-word;">
    <https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2768923>
  </div>
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    <img src="data:image/png;base64,#paltiel-model.png" alt="diagonal layout" width="100%"/>
    <img src="data:image/png;base64,#paltiel-iso-dorm.png" alt="diagonal layout" width="100%"/>
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# SARS-CoV-2 Screening Strategies

**Project Idea**: "*Can we implement an interactive dashboard with improved accessibility and ease of use.*"

**Audience**:
  - University of Wisconsin-Madison campus leaders
  - Wisconsin public health officials
  - Health system officials
  - Interested modelers

]

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# SARS-CoV-2 Screening Strategies

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- Calculate minimum performance attributes of a SARS-CoV-2 monitoring program

- Suggest what isolation and treatment capacity would need to be in place

- Forecast what testing might cost

- Recommended by the authors of the paper

- Website: [data-viz.it.wisc.edu/covid-19-screening/](https://data-viz.it.wisc.edu/covid-19-screening/)

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# Nowcast COVID-19 Cases and Hospitalizations

**Project Idea**:
- Nowcast cases by HERC regions
- Nowcast hospitalizations by HERC regions
- View time series
- View coverage of credible intervals

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**Audience**:
- Wisconsin public health officials
- Health system officials
- Interested modelers

]

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# Nowcast COVID-19 Cases and Hospitalizations

.pull-left[
  <center>
  <img src="cases.png" height="200" border = "1">
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.center[
  </br>
  [https://data-viz.it.wisc.edu/cases-r-hosp-geofacet-wi-region/](https://data-viz.it.wisc.edu/cases-r-hosp-geofacet-wi-region/)
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# Publish Datasets

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- Daily updates to new data

- Customized to the needs of the public heath system

- Publishes data, models, and other R objects

- Easy to share across projects and with users

- Automatically versioned

- Track changes, re-run analyses on historical data, and undo mistakes

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# **Cow Break!**

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# Automate DairyCOMP 305

Emil Walleser & D&ouml;rte D&ouml;pfer (University of Wisconsin-Madison)

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# DairyCOMP 305

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# Motivation

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- Health data is locked in DairyCOMP 305

- Limited integrated analysis

- Extensive preprocessing

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# DairyCOMP 305

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# Automate DairyCOMP 305

**Project Idea**:
- Automate DairyCOMP 305 write out
- Apply tools to support data-driven decisions
- Customize reports and graphs for a better management experience

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**Audience**:
- DairyCOMP 305 users
- Dairy Skills I instructors & students

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# Dairy Co-Pilot

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- Simplify data wrangling in DairyCOMP 305

- Reduce time for data cleaning

- Simplify analysis

- Enhance analysis

- Website: [connect.doit.wisc.edu/dairy-copilot/](https://connect.doit.wisc.edu/dairy-copilot/)

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# Update DDCheck App

D&ouml;rte D&ouml;pfer (University of Wisconsin-Madison)

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# DDCheck App

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# Update DDCheck App

**Project Idea**:
  - Update DDCheck user interface
  - Apply computer vision tools to support data-driven decisions
  - Customize reports and graphs for a better management experience

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**Audience**:
  - Veterinarians, hoof trimmers, farmers, and herd managers
  - Instructors and students

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# DDCheckPlus App

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- Simplify data recording

- Reduce time for data analysis

- Simplify analysis

- Enhance analysis

- Website: [connect.doit.wisc.edu/dd-check/](https://connect.doit.wisc.edu/dd-check/)

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# DD Detection Module

- Computer vision aided data recording

- YOLOv5s Core ML model on iOS/iPadOS device

- Fast with sufficient accuracy

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# R Shiny App

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- Machine learning assisted data analysis

- Predict prevalence of disease in its various stages

- User-friendly web application

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# Update DDCheck App

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# Presentation Application

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# **Thank You!**

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    Contact: <a href = "mailto: aravamuthan@wisc.edu">aravamuthan@wisc.edu</a>
    </br>
    Website: <a href = "https://connect.doit.wisc.edu/posit-day/">connect.doit.wisc.edu/posit-day/</a>
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